HEADER TRANSFERASE 06-JAN-23 8C56 TITLE CPG SPECIFIC M.MPEI METHYLTRANSFERASE CRYSTALLIZED IN THE PRESENCE OF TITLE 2 2'-DEOXY-5-METHYLZEBULARINE (5MZ) AND 5-METHYLCYTOSINE CONTAINING TITLE 3 DSDNA COMPND MOL_ID: 1; COMPND 2 MOLECULE: CYTOSINE-SPECIFIC METHYLTRANSFERASE; COMPND 3 CHAIN: A; COMPND 4 ENGINEERED: YES; COMPND 5 MOL_ID: 2; COMPND 6 MOLECULE: DNA (5'-D(*CP*CP*AP*CP*AP*TP*GP*(5PY)P*GP*CP*TP*GP*AP*A)- COMPND 7 3'); COMPND 8 CHAIN: B; COMPND 9 ENGINEERED: YES; COMPND 10 MOL_ID: 3; COMPND 11 MOLECULE: DNA (5'-D(*GP*TP*TP*CP*AP*GP*(5CM)P*GP*CP*AP*TP*GP*TP*G)- COMPND 12 3'); COMPND 13 CHAIN: C; COMPND 14 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: MALACOPLASMA PENETRANS HF-2; SOURCE 3 ORGANISM_TAXID: 272633; SOURCE 4 STRAIN: HF-2; SOURCE 5 GENE: MYPE4940; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 7 EXPRESSION_SYSTEM_TAXID: 562; SOURCE 8 EXPRESSION_SYSTEM_STRAIN: 2566; SOURCE 9 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 10 EXPRESSION_SYSTEM_PLASMID: PET-28A; SOURCE 11 MOL_ID: 2; SOURCE 12 ORGANISM_SCIENTIFIC: SYNTHETIC CONSTRUCT; SOURCE 13 ORGANISM_TAXID: 32630; SOURCE 14 EXPRESSION_SYSTEM: SYNTHETIC CONSTRUCT; SOURCE 15 EXPRESSION_SYSTEM_TAXID: 32630; SOURCE 16 MOL_ID: 3; SOURCE 17 ORGANISM_SCIENTIFIC: SYNTHETIC CONSTRUCT; SOURCE 18 ORGANISM_TAXID: 32630; SOURCE 19 EXPRESSION_SYSTEM: SYNTHETIC CONSTRUCT; SOURCE 20 EXPRESSION_SYSTEM_TAXID: 32630 KEYWDS M.MPEI, DNA METHYLTRANSFERASE, DNA, 5-METHYLCYTOSINE, 5-METHYL- KEYWDS 2 ZEBULARINE, 5MZ, 5MZEB, 5MC, CPG, TRANSFERASE EXPDTA X-RAY DIFFRACTION AUTHOR M.WOJCIECHOWSKI,H.CZAPINSKA,J.KRWAWICZ,D.RAFALSKI,M.BOCHTLER REVDAT 3 04-SEP-24 8C56 1 JRNL REVDAT 2 17-JUL-24 8C56 1 JRNL REVDAT 1 17-JAN-24 8C56 0 JRNL AUTH M.WOJCIECHOWSKI,H.CZAPINSKA,J.KRWAWICZ,D.RAFALSKI,M.BOCHTLER JRNL TITL CYTOSINE ANALOGUES AS DNA METHYLTRANSFERASE SUBSTRATES. JRNL REF NUCLEIC ACIDS RES. V. 52 9267 2024 JRNL REFN ESSN 1362-4962 JRNL PMID 38966999 JRNL DOI 10.1093/NAR/GKAE568 REMARK 1 REMARK 1 REFERENCE 1 REMARK 1 AUTH M.WOJCIECHOWSKI,H.CZAPINSKA,M.BOCHTLER REMARK 1 TITL CPG UNDERREPRESENTATION AND THE BACTERIAL CPG-SPECIFIC DNA REMARK 1 TITL 2 METHYLTRANSFERASE M.MPEI. REMARK 1 REF PROC. NATL. ACAD. SCI. V. 110 105 2013 REMARK 1 REF 2 U.S.A. REMARK 1 REFN ESSN 1091-6490 REMARK 1 PMID 23248272 REMARK 1 DOI 10.1073/PNAS.1207986110 REMARK 1 REFERENCE 2 REMARK 1 AUTH J.SONG,M.TEPLOVA,S.ISHIBE-MURAKAMI,D.J.PATEL REMARK 1 TITL STRUCTURE-BASED MECHANISTIC INSIGHTS INTO DNMT1-MEDIATED REMARK 1 TITL 2 MAINTENANCE DNA METHYLATION. REMARK 1 REF SCIENCE V. 335 709 2012 REMARK 1 REFN ESSN 1095-9203 REMARK 1 PMID 22323818 REMARK 1 DOI 10.1126/SCIENCE.1214453 REMARK 2 REMARK 2 RESOLUTION. 2.40 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : REFMAC 5.8.0258 REMARK 3 AUTHORS : MURSHUDOV,SKUBAK,LEBEDEV,PANNU,STEINER, REMARK 3 : NICHOLLS,WINN,LONG,VAGIN REMARK 3 REMARK 3 REFINEMENT TARGET : MAXIMUM LIKELIHOOD REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 2.40 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 19.89 REMARK 3 DATA CUTOFF (SIGMA(F)) : NULL REMARK 3 COMPLETENESS FOR RANGE (%) : 99.6 REMARK 3 NUMBER OF REFLECTIONS : 23997 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 CROSS-VALIDATION METHOD : THROUGHOUT REMARK 3 FREE R VALUE TEST SET SELECTION : RANDOM REMARK 3 R VALUE (WORKING + TEST SET) : 0.175 REMARK 3 R VALUE (WORKING SET) : 0.173 REMARK 3 FREE R VALUE : 0.216 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.000 REMARK 3 FREE R VALUE TEST SET COUNT : 1253 REMARK 3 REMARK 3 FIT IN THE HIGHEST RESOLUTION BIN. REMARK 3 TOTAL NUMBER OF BINS USED : NULL REMARK 3 BIN RESOLUTION RANGE HIGH (A) : 2.40 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 2.46 REMARK 3 REFLECTION IN BIN (WORKING SET) : 1644 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 97.64 REMARK 3 BIN R VALUE (WORKING SET) : 0.3160 REMARK 3 BIN FREE R VALUE SET COUNT : 94 REMARK 3 BIN FREE R VALUE : 0.4020 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 3199 REMARK 3 NUCLEIC ACID ATOMS : 569 REMARK 3 HETEROGEN ATOMS : 33 REMARK 3 SOLVENT ATOMS : 412 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 53.30 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 51.84 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : 0.58000 REMARK 3 B22 (A**2) : 0.58000 REMARK 3 B33 (A**2) : -1.16000 REMARK 3 B12 (A**2) : 0.00000 REMARK 3 B13 (A**2) : 0.00000 REMARK 3 B23 (A**2) : 0.00000 REMARK 3 REMARK 3 ESTIMATED OVERALL COORDINATE ERROR. REMARK 3 ESU BASED ON R VALUE (A): 0.362 REMARK 3 ESU BASED ON FREE R VALUE (A): 0.228 REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): 0.191 REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): 20.142 REMARK 3 REMARK 3 CORRELATION COEFFICIENTS. REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.966 REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.947 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES COUNT RMS WEIGHT REMARK 3 BOND LENGTHS REFINED ATOMS (A): 4220 ; 0.009 ; 0.018 REMARK 3 BOND LENGTHS OTHERS (A): 3784 ; 0.001 ; 0.020 REMARK 3 BOND ANGLES REFINED ATOMS (DEGREES): 5831 ; 1.006 ; 1.846 REMARK 3 BOND ANGLES OTHERS (DEGREES): 8788 ; 0.795 ; 3.000 REMARK 3 TORSION ANGLES, PERIOD 1 (DEGREES): 443 ; 5.523 ; 5.000 REMARK 3 TORSION ANGLES, PERIOD 2 (DEGREES): 175 ;38.755 ;25.429 REMARK 3 TORSION ANGLES, PERIOD 3 (DEGREES): 713 ;14.346 ;15.000 REMARK 3 TORSION ANGLES, PERIOD 4 (DEGREES): 14 ;14.394 ;15.000 REMARK 3 CHIRAL-CENTER RESTRAINTS (A**3): 598 ; 0.060 ; 0.200 REMARK 3 GENERAL PLANES REFINED ATOMS (A): 4482 ; 0.003 ; 0.020 REMARK 3 GENERAL PLANES OTHERS (A): 979 ; 0.001 ; 0.020 REMARK 3 NON-BONDED CONTACTS REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 NON-BONDED CONTACTS OTHERS (A): NULL ; NULL ; NULL REMARK 3 NON-BONDED TORSION REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 NON-BONDED TORSION OTHERS (A): NULL ; NULL ; NULL REMARK 3 H-BOND (X...Y) REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 H-BOND (X...Y) OTHERS (A): NULL ; NULL ; NULL REMARK 3 POTENTIAL METAL-ION REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 POTENTIAL METAL-ION OTHERS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY VDW REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY VDW OTHERS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY H-BOND REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY H-BOND OTHERS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY METAL-ION REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY METAL-ION OTHERS (A): NULL ; NULL ; NULL REMARK 3 REMARK 3 ISOTROPIC THERMAL FACTOR RESTRAINTS. COUNT RMS WEIGHT REMARK 3 MAIN-CHAIN BOND REFINED ATOMS (A**2): 1697 ; 0.646 ; 3.084 REMARK 3 MAIN-CHAIN BOND OTHER ATOMS (A**2): 1696 ; 0.643 ; 3.084 REMARK 3 MAIN-CHAIN ANGLE REFINED ATOMS (A**2): 2165 ; 1.187 ; 4.620 REMARK 3 MAIN-CHAIN ANGLE OTHER ATOMS (A**2): 2166 ; 1.187 ; 4.622 REMARK 3 SIDE-CHAIN BOND REFINED ATOMS (A**2): 2523 ; 0.520 ; 3.131 REMARK 3 SIDE-CHAIN BOND OTHER ATOMS (A**2): 2523 ; 0.520 ; 3.131 REMARK 3 SIDE-CHAIN ANGLE REFINED ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN ANGLE OTHER ATOMS (A**2): 3667 ; 0.951 ; 4.667 REMARK 3 LONG RANGE B REFINED ATOMS (A**2): 5377 ; 3.770 ;35.309 REMARK 3 LONG RANGE B OTHER ATOMS (A**2): 5193 ; 3.279 ;34.612 REMARK 3 REMARK 3 ANISOTROPIC THERMAL FACTOR RESTRAINTS. COUNT RMS WEIGHT REMARK 3 RIGID-BOND RESTRAINTS (A**2): NULL ; NULL ; NULL REMARK 3 SPHERICITY; FREE ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SPHERICITY; BONDED ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 REMARK 3 NCS RESTRAINTS STATISTICS REMARK 3 NUMBER OF DIFFERENT NCS GROUPS : NULL REMARK 3 REMARK 3 TLS DETAILS REMARK 3 NUMBER OF TLS GROUPS : 1 REMARK 3 REMARK 3 TLS GROUP : 1 REMARK 3 NUMBER OF COMPONENTS GROUP : 3 REMARK 3 COMPONENTS C SSSEQI TO C SSSEQI REMARK 3 RESIDUE RANGE : A 6 A 393 REMARK 3 RESIDUE RANGE : B 1 B 14 REMARK 3 RESIDUE RANGE : C 1 C 14 REMARK 3 ORIGIN FOR THE GROUP (A): 22.6920 22.2140 46.1400 REMARK 3 T TENSOR REMARK 3 T11: 0.1308 T22: 0.2595 REMARK 3 T33: 0.0070 T12: -0.0402 REMARK 3 T13: -0.0048 T23: 0.0382 REMARK 3 L TENSOR REMARK 3 L11: 0.9840 L22: 2.2783 REMARK 3 L33: 1.1521 L12: 1.0124 REMARK 3 L13: 0.1000 L23: 0.2051 REMARK 3 S TENSOR REMARK 3 S11: 0.0811 S12: -0.1767 S13: -0.0331 REMARK 3 S21: -0.0025 S22: -0.0724 S23: 0.0073 REMARK 3 S31: 0.0033 S32: 0.1247 S33: -0.0086 REMARK 3 REMARK 3 BULK SOLVENT MODELLING. REMARK 3 METHOD USED : MASK REMARK 3 PARAMETERS FOR MASK CALCULATION REMARK 3 VDW PROBE RADIUS : 1.20 REMARK 3 ION PROBE RADIUS : 0.80 REMARK 3 SHRINKAGE RADIUS : 0.80 REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: REMARK 3 HYDROGEN ATOMS HAVE BEEN ADDED IN THE RIDING POSITIONS. REMARK 3 U VALUES : WITH TLS ADDED. REMARK 3 IONS AND SOLVENT MOLECULES HAVE BEEN MODELLED TENTATIVELY. REMARK 3 S-ADENOSYLHOMOCYSTEINE (SAH) HAS BEEN MODELLED IN THE CO-SUBSTRATE REMARK 3 BINDING POCKET BUT ONLY PARTS OF THE MOLECULE CORRESPONDING TO ITS REMARK 3 BASE AND AMINO ACID END ARE RESOLVED IN THE ELECTRON DENSITY. THE REMARK 3 CENTRAL PART OF THE CO-PRODUCT COULD NOT BE UNAMBIGUOUSLY TRACED, REMARK 3 WHICH MAY BE DUE TO THE DECOMPOSITION OF THE CO-SUBSTRATE S- REMARK 3 ADENOSYLMETHIONINE (SAM) USED FOR CRYSTALLIZATION TO HOMOSERINE REMARK 3 LACTONE (HSL) AND METHYLTHIOADENOSINE (MTA). REMARK 3 THE DISTANCE BETWEEN THE CATALYTIC CYSTEINE (CYS135) OF THE REMARK 3 PROTEIN AND THE C6 ATOM OF THE SUBSTRATE BASE IS BETWEEN A REMARK 3 COVALENT AND NON-COVALENT BOND AND HAS NOT BEEN CONSTRAINED DURING REMARK 3 THE REFINEMENT. REMARK 4 REMARK 4 8C56 COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBE ON 06-JAN-23. REMARK 100 THE DEPOSITION ID IS D_1292110462. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 01-FEB-13 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 5.6 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : BESSY REMARK 200 BEAMLINE : 14.1 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.918409 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : PIXEL REMARK 200 DETECTOR MANUFACTURER : DECTRIS PILATUS 6M REMARK 200 INTENSITY-INTEGRATION SOFTWARE : XDS REMARK 200 DATA SCALING SOFTWARE : XDS REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 25251 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.400 REMARK 200 RESOLUTION RANGE LOW (A) : 20.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 99.6 REMARK 200 DATA REDUNDANCY : 8.600 REMARK 200 R MERGE (I) : NULL REMARK 200 R SYM (I) : 0.11400 REMARK 200 FOR THE DATA SET : 16.8900 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.40 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.54 REMARK 200 COMPLETENESS FOR SHELL (%) : 99.0 REMARK 200 DATA REDUNDANCY IN SHELL : 8.80 REMARK 200 R MERGE FOR SHELL (I) : NULL REMARK 200 R SYM FOR SHELL (I) : 1.20300 REMARK 200 FOR SHELL : 2.050 REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MOLECULAR REPLACEMENT REMARK 200 SOFTWARE USED: REFMAC REMARK 200 STARTING MODEL: 4DKJ REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 56.16 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.81 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 10% PEG 3350, 150 MM NACL, 50 MM REMARK 280 SODIUM CITRATE (FINAL PH, 5.6). FOR CRYOPROTECTION GLYCEROL WAS REMARK 280 ADDED TO 25% V/V, PH 5.6, VAPOR DIFFUSION, SITTING DROP, REMARK 280 TEMPERATURE 294K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 41 21 2 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -X,-Y,Z+1/2 REMARK 290 3555 -Y+1/2,X+1/2,Z+1/4 REMARK 290 4555 Y+1/2,-X+1/2,Z+3/4 REMARK 290 5555 -X+1/2,Y+1/2,-Z+1/4 REMARK 290 6555 X+1/2,-Y+1/2,-Z+3/4 REMARK 290 7555 Y,X,-Z REMARK 290 8555 -Y,-X,-Z+1/2 REMARK 290 REMARK 290 WHERE NNN -> OPERATOR NUMBER REMARK 290 MMM -> TRANSLATION VECTOR REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY TRANSFORMATIONS REMARK 290 THE FOLLOWING TRANSFORMATIONS OPERATE ON THE ATOM/HETATM REMARK 290 RECORDS IN THIS ENTRY TO PRODUCE CRYSTALLOGRAPHICALLY REMARK 290 RELATED MOLECULES. REMARK 290 SMTRY1 1 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 1 0.000000 1.000000 0.000000 0.00000 REMARK 290 SMTRY3 1 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY1 2 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 2 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 86.94150 REMARK 290 SMTRY1 3 0.000000 -1.000000 0.000000 42.12950 REMARK 290 SMTRY2 3 1.000000 0.000000 0.000000 42.12950 REMARK 290 SMTRY3 3 0.000000 0.000000 1.000000 43.47075 REMARK 290 SMTRY1 4 0.000000 1.000000 0.000000 42.12950 REMARK 290 SMTRY2 4 -1.000000 0.000000 0.000000 42.12950 REMARK 290 SMTRY3 4 0.000000 0.000000 1.000000 130.41225 REMARK 290 SMTRY1 5 -1.000000 0.000000 0.000000 42.12950 REMARK 290 SMTRY2 5 0.000000 1.000000 0.000000 42.12950 REMARK 290 SMTRY3 5 0.000000 0.000000 -1.000000 43.47075 REMARK 290 SMTRY1 6 1.000000 0.000000 0.000000 42.12950 REMARK 290 SMTRY2 6 0.000000 -1.000000 0.000000 42.12950 REMARK 290 SMTRY3 6 0.000000 0.000000 -1.000000 130.41225 REMARK 290 SMTRY1 7 0.000000 1.000000 0.000000 0.00000 REMARK 290 SMTRY2 7 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY3 7 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY1 8 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY2 8 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY3 8 0.000000 0.000000 -1.000000 86.94150 REMARK 290 REMARK 290 REMARK: NULL REMARK 300 REMARK 300 BIOMOLECULE: 1 REMARK 300 SEE REMARK 350 FOR THE AUTHOR PROVIDED AND/OR PROGRAM REMARK 300 GENERATED ASSEMBLY INFORMATION FOR THE STRUCTURE IN REMARK 300 THIS ENTRY. THE REMARK MAY ALSO PROVIDE INFORMATION ON REMARK 300 BURIED SURFACE AREA. REMARK 350 REMARK 350 COORDINATES FOR A COMPLETE MULTIMER REPRESENTING THE KNOWN REMARK 350 BIOLOGICALLY SIGNIFICANT OLIGOMERIZATION STATE OF THE REMARK 350 MOLECULE CAN BE GENERATED BY APPLYING BIOMT TRANSFORMATIONS REMARK 350 GIVEN BELOW. BOTH NON-CRYSTALLOGRAPHIC AND REMARK 350 CRYSTALLOGRAPHIC OPERATIONS ARE GIVEN. REMARK 350 REMARK 350 BIOMOLECULE: 1 REMARK 350 AUTHOR DETERMINED BIOLOGICAL UNIT: TRIMERIC REMARK 350 APPLY THE FOLLOWING TO CHAINS: A, B, C REMARK 350 BIOMT1 1 1.000000 0.000000 0.000000 0.00000 REMARK 350 BIOMT2 1 0.000000 1.000000 0.000000 0.00000 REMARK 350 BIOMT3 1 0.000000 0.000000 1.000000 0.00000 REMARK 375 REMARK 375 SPECIAL POSITION REMARK 375 THE FOLLOWING ATOMS ARE FOUND TO BE WITHIN 0.15 ANGSTROMS REMARK 375 OF A SYMMETRY RELATED ATOM AND ARE ASSUMED TO BE ON SPECIAL REMARK 375 POSITIONS. REMARK 375 REMARK 375 ATOM RES CSSEQI REMARK 375 HOH A 765 LIES ON A SPECIAL POSITION. REMARK 465 REMARK 465 MISSING RESIDUES REMARK 465 THE FOLLOWING RESIDUES WERE NOT LOCATED IN THE REMARK 465 EXPERIMENT. (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN REMARK 465 IDENTIFIER; SSSEQ=SEQUENCE NUMBER; I=INSERTION CODE.) REMARK 465 REMARK 465 M RES C SSSEQI REMARK 465 MET A 1 REMARK 465 ASN A 2 REMARK 465 SER A 3 REMARK 465 ASN A 4 REMARK 465 LYS A 5 REMARK 465 GLU A 394 REMARK 465 GLU A 395 REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: TORSION ANGLES REMARK 500 REMARK 500 TORSION ANGLES OUTSIDE THE EXPECTED RAMACHANDRAN REGIONS: REMARK 500 (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN IDENTIFIER; REMARK 500 SSEQ=SEQUENCE NUMBER; I=INSERTION CODE). REMARK 500 REMARK 500 STANDARD TABLE: REMARK 500 FORMAT:(10X,I3,1X,A3,1X,A1,I4,A1,4X,F7.2,3X,F7.2) REMARK 500 REMARK 500 EXPECTED VALUES: GJ KLEYWEGT AND TA JONES (1996). PHI/PSI- REMARK 500 CHOLOGY: RAMACHANDRAN REVISITED. STRUCTURE 4, 1395 - 1400 REMARK 500 REMARK 500 M RES CSSEQI PSI PHI REMARK 500 LYS A 7 36.51 -89.78 REMARK 500 SER A 80 -10.96 81.04 REMARK 500 PHE A 112 -66.26 74.87 REMARK 500 CYS A 225 32.15 -98.54 REMARK 500 ASN A 290 11.57 80.87 REMARK 500 ARG A 326 71.03 -112.28 REMARK 500 REMARK 500 REMARK: NULL REMARK 620 REMARK 620 METAL COORDINATION REMARK 620 (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN IDENTIFIER; REMARK 620 SSEQ=SEQUENCE NUMBER; I=INSERTION CODE): REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 NA C 101 NA REMARK 620 N RES CSSEQI ATOM REMARK 620 1 DG C 1 O6 REMARK 620 2 HOH C 213 O 71.9 REMARK 620 3 HOH C 225 O 95.0 146.1 REMARK 620 N 1 2 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 4DKJ RELATED DB: PDB REMARK 900 M.MPEI METHYLTRANSFERASE IN COMPLEX WITH 5FC/5MC CONTAINING TARGET REMARK 900 DNA REMARK 900 RELATED ID: 4DA4 RELATED DB: PDB REMARK 900 MOUSE DNMT1 (731-1602) BOUND TO HEMIMETHYLATED CPG DNA DBREF 8C56 A 1 395 UNP Q8EVR5 Q8EVR5_MALP2 1 395 DBREF 8C56 B 1 14 PDB 8C56 8C56 1 14 DBREF 8C56 C 1 14 PDB 8C56 8C56 1 14 SEQADV 8C56 ARG A 68 UNP Q8EVR5 GLN 68 CONFLICT SEQADV 8C56 ARG A 71 UNP Q8EVR5 LYS 71 CONFLICT SEQADV 8C56 PRO A 295 UNP Q8EVR5 SER 295 CONFLICT SEQRES 1 A 395 MET ASN SER ASN LYS ASP LYS ILE LYS VAL ILE LYS VAL SEQRES 2 A 395 PHE GLU ALA PHE ALA GLY ILE GLY SER GLN PHE LYS ALA SEQRES 3 A 395 LEU LYS ASN ILE ALA ARG SER LYS ASN TRP GLU ILE GLN SEQRES 4 A 395 HIS SER GLY MET VAL GLU TRP PHE VAL ASP ALA ILE VAL SEQRES 5 A 395 SER TYR VAL ALA ILE HIS SER LYS ASN PHE ASN PRO LYS SEQRES 6 A 395 ILE GLU ARG LEU ASP ARG ASP ILE LEU SER ILE SER ASN SEQRES 7 A 395 ASP SER LYS MET PRO ILE SER GLU TYR GLY ILE LYS LYS SEQRES 8 A 395 ILE ASN ASN THR ILE LYS ALA SER TYR LEU ASN TYR ALA SEQRES 9 A 395 LYS LYS HIS PHE ASN ASN LEU PHE ASP ILE LYS LYS VAL SEQRES 10 A 395 ASN LYS ASP ASN PHE PRO LYS ASN ILE ASP ILE PHE THR SEQRES 11 A 395 TYR SER PHE PRO CYS GLN ASP LEU SER VAL GLN GLY LEU SEQRES 12 A 395 GLN LYS GLY ILE ASP LYS GLU LEU ASN THR ARG SER GLY SEQRES 13 A 395 LEU LEU TRP GLU ILE GLU ARG ILE LEU GLU GLU ILE LYS SEQRES 14 A 395 ASN SER PHE SER LYS GLU GLU MET PRO LYS TYR LEU LEU SEQRES 15 A 395 MET GLU ASN VAL LYS ASN LEU LEU SER HIS LYS ASN LYS SEQRES 16 A 395 LYS ASN TYR ASN THR TRP LEU LYS GLN LEU GLU LYS PHE SEQRES 17 A 395 GLY TYR LYS SER LYS THR TYR LEU LEU ASN SER LYS ASN SEQRES 18 A 395 PHE ASP ASN CYS GLN ASN ARG GLU ARG VAL PHE CYS LEU SEQRES 19 A 395 SER ILE ARG ASP ASP TYR LEU GLU LYS THR GLY PHE LYS SEQRES 20 A 395 PHE LYS GLU LEU GLU LYS VAL LYS ASN PRO PRO LYS LYS SEQRES 21 A 395 ILE LYS ASP ILE LEU VAL ASP SER SER ASN TYR LYS TYR SEQRES 22 A 395 LEU ASN LEU ASN LYS TYR GLU THR THR THR PHE ARG GLU SEQRES 23 A 395 THR LYS SER ASN ILE ILE SER ARG PRO LEU LYS ASN TYR SEQRES 24 A 395 THR THR PHE ASN SER GLU ASN TYR VAL TYR ASN ILE ASN SEQRES 25 A 395 GLY ILE GLY PRO THR LEU THR ALA SER GLY ALA ASN SER SEQRES 26 A 395 ARG ILE LYS ILE GLU THR GLN GLN GLY VAL ARG TYR LEU SEQRES 27 A 395 THR PRO LEU GLU CYS PHE LYS TYR MET GLN PHE ASP VAL SEQRES 28 A 395 ASN ASP PHE LYS LYS VAL GLN SER THR ASN LEU ILE SER SEQRES 29 A 395 GLU ASN LYS MET ILE TYR ILE ALA GLY ASN SER ILE PRO SEQRES 30 A 395 VAL LYS ILE LEU GLU ALA ILE PHE ASN THR LEU GLU PHE SEQRES 31 A 395 VAL ASN ASN GLU GLU SEQRES 1 B 14 DC DC DA DC DA DT DG 5PY DG DC DT DG DA SEQRES 2 B 14 DA SEQRES 1 C 14 DG DT DT DC DA DG 5CM DG DC DA DT DG DT SEQRES 2 C 14 DG HET 5PY B 8 19 HET 5CM C 7 20 HET SAH A 401 26 HET GOL A 402 6 HET NA C 101 1 HETNAM 5PY 1-(2'-DEOXY-5'-O-PHOSPHONO-BETA-D-ERYTHRO- HETNAM 2 5PY PENTOFURANOSYL)-5-METHYLPYRIMIDIN-2(1H)-ONE HETNAM 5CM 5-METHYL-2'-DEOXY-CYTIDINE-5'-MONOPHOSPHATE HETNAM SAH S-ADENOSYL-L-HOMOCYSTEINE HETNAM GOL GLYCEROL HETNAM NA SODIUM ION HETSYN GOL GLYCERIN; PROPANE-1,2,3-TRIOL FORMUL 2 5PY C10 H15 N2 O7 P FORMUL 3 5CM C10 H16 N3 O7 P FORMUL 4 SAH C14 H20 N6 O5 S FORMUL 5 GOL C3 H8 O3 FORMUL 6 NA NA 1+ FORMUL 7 HOH *412(H2 O) HELIX 1 AA1 GLY A 21 ASN A 35 1 15 HELIX 2 AA2 PHE A 47 SER A 59 1 13 HELIX 3 AA3 SER A 85 ASN A 93 1 9 HELIX 4 AA4 THR A 95 ASN A 109 1 15 HELIX 5 AA5 ASP A 113 VAL A 117 5 5 HELIX 6 AA6 ASP A 148 ASN A 152 5 5 HELIX 7 AA7 ARG A 154 GLY A 156 5 3 HELIX 8 AA8 LEU A 157 PHE A 172 1 16 HELIX 9 AA9 SER A 173 MET A 177 5 5 HELIX 10 AB1 ASN A 188 LEU A 190 5 3 HELIX 11 AB2 SER A 191 PHE A 208 1 18 HELIX 12 AB3 LYS A 220 PHE A 222 5 3 HELIX 13 AB4 ASP A 238 GLY A 245 1 8 HELIX 14 AB5 GLU A 250 VAL A 254 5 5 HELIX 15 AB6 LYS A 260 LEU A 265 5 6 HELIX 16 AB7 PHE A 302 GLU A 305 5 4 HELIX 17 AB8 GLY A 322 ARG A 326 5 5 HELIX 18 AB9 THR A 339 MET A 347 1 9 HELIX 19 AC1 ASP A 350 THR A 360 1 11 HELIX 20 AC2 SER A 364 ASN A 374 1 11 HELIX 21 AC3 PRO A 377 THR A 387 1 11 SHEET 1 AA1 6 TRP A 36 VAL A 44 0 SHEET 2 AA1 6 LYS A 9 ALA A 16 1 N ILE A 11 O GLN A 39 SHEET 3 AA1 6 ILE A 128 TYR A 131 1 O ILE A 128 N PHE A 14 SHEET 4 AA1 6 TYR A 180 VAL A 186 1 O LEU A 182 N TYR A 131 SHEET 5 AA1 6 GLU A 229 ARG A 237 -1 O SER A 235 N LEU A 181 SHEET 6 AA1 6 TYR A 210 ASN A 218 -1 N TYR A 215 O PHE A 232 SHEET 1 AA2 5 ARG A 285 GLU A 286 0 SHEET 2 AA2 5 ILE A 292 PRO A 295 -1 O SER A 293 N ARG A 285 SHEET 3 AA2 5 TYR A 307 ASN A 310 -1 O ASN A 310 N ILE A 292 SHEET 4 AA2 5 LYS A 328 THR A 331 1 O LYS A 328 N TYR A 309 SHEET 5 AA2 5 GLY A 334 TYR A 337 -1 O ARG A 336 N ILE A 329 LINK O3' DG B 7 P 5PY B 8 1555 1555 1.60 LINK O3' 5PY B 8 P DG B 9 1555 1555 1.60 LINK O3' DG C 6 P 5CM C 7 1555 1555 1.60 LINK O3' 5CM C 7 P DG C 8 1555 1555 1.60 LINK O6 DG C 1 NA NA C 101 1555 1555 2.94 LINK NA NA C 101 O HOH C 213 1555 1555 2.74 LINK NA NA C 101 O HOH C 225 1555 4554 3.16 CRYST1 84.259 84.259 173.883 90.00 90.00 90.00 P 41 21 2 8 ORIGX1 1.000000 0.000000 0.000000 0.00000 ORIGX2 0.000000 1.000000 0.000000 0.00000 ORIGX3 0.000000 0.000000 1.000000 0.00000 SCALE1 0.011868 0.000000 0.000000 0.00000 SCALE2 0.000000 0.011868 0.000000 0.00000 SCALE3 0.000000 0.000000 0.005751 0.00000